Most BIOSs have an option to change the drive that the system boots from - normally C:, the primary drive on the 1st IDE channel (eg, most BIOSs allow this to be changed to A: to boot from floppy, CDROM to boot from CD, SCSI to boot from SCSI disks, etc). Have you tried to change this to D: (or whatever letter is being assigned to the raid array), or EXT (external adapter, such as your raid controller)? Some motherboards have an additional option to specify what EXT means (on my Abit BP6, I can set it to the on-board HPT UDMA66 adapter, or SCSI/additional adapter card).
By the way, I don't think there is a permanant way to change the drive letters for your system drive in software, it's down to BIOS settings/hardware configuration.